Biology subjects

Block, B. A.

Publications and source records attributed to Block, B. A..

3 recordsLinked to original sources

bioRxiv2025

Whole Genome Assembly of the Atlantic Bluefin Tuna Thunnus thynnus, with Phased Haplotypes

Atlantic bluefin tuna (Thunnus thynnus) are highly migratory fish, the largest tuna in the genus Thunnus. These fish possess a unique suite of traits, including regional endothermy, in their swimming muscle, viscera, brain and eyes that elevates tissue temperatures significantly above ambient water temperatures. Bluefin tuna also have an efficient thunniform locomotory style, involving a fusiform low drag external shape and a novel musculoskeletal system that enhances elastic energy storage. Together the unique swimming form and warm muscle temperatures enable this species to move across large expanses of the ocean. Atlantic bluefin tuna are targeted by high-value international fisheries of over fifty nations. Populations have recovered in recent years and the species is now actively farmed extensively within the Mediterranean Sea and eastern Atlantic. To date, fisheries management and evolutionary studies have been hampered by a lack of genomic resources. Here, we report a novel de novo chromosome-level phased genome assembly for the Atlantic bluefin tuna obtained using PacBio HiFi reads and Dovetail Omni-C scaffolding. This assembly was scaffolded into 24 chromosomes containing 98% of the genes in the BUSCO reference dataset, demonstrating a high level of contiguity with a contig N50 of 26.54 and assembly size of [~]800Mbp. We compare a diploid-resolved (2N) genome assembly of Atlantic bluefin tuna with a haplotype-collapsed (1N) genome assembly from a Pacific bluefin tuna caught in the eastern Pacific off California. We show the two species have a 98.47% sequence identity. These high-quality genomes for northern bluefin tunas provide the genomic tools necessary for improving phylogenomic and evolutionary physiology analyses of this lineage and are important for potential functional assays for population biology of these commercially important species.

evolutionary biology↗

bioRxiv2025

Mapping Risk and Resilience Across Indo-Pacific Reefs with Shark Genomescapes

Overfishing has severely depleted marine populations worldwide, including within protected areas. Illegal and unreported fishing are major contributors to this decline. Large-bodied apex predators such as sharks are among the most affected, with overfishing causing dramatic species declines and ecosystem destabilization due to trophic downgrading. Key barriers to effective marine conservation and management include: Data deficiencies that hinder population benchmarks and impact assessments, limited surveillance, allowing illegal fisheries to disproportionately affect apex predators, and insufficient capacity in vulnerable nations to monitor and protect species within their waters. Our study addresses these challenges through a novel genomic framework that enables assessment of shark population diversity and health, while also improving fisheries traceability by detecting instances of illegal fishing across the Indian and Pacific Oceans. We present the Reefshark Genomescape, the first genome-wide reference database for Indo-Pacific reef sharks, an assessment of genetic diversity, structure, and connectivity of two key species across their Indo-Pacific range and geographic assignment of fished individuals using population-specific genetic signatures. We show that grey reef shark (Carcharhinus amblyrhynchos) populations exhibit high genetic diversity, strong population structure, and elevated Fst values, with previously unknown connectivity between the central and western Indian Ocean and clear isolation of populations in the Andaman Sea. In contrast, silvertip sharks (Carcharhinus albimarginatus) display high connectivity, but show genomic signals of declining population health, supporting a reassessment of their IUCN status. Using supervised machine learning with Monte Carlo cross-validation, we assigned geographic origins to fished grey reef sharks with 96% accuracy. These findings provide critical insights into population structure, connectivity, and health of two ecologically important reef shark species, while establishing a robust method for assigning geographic origin. We anticipate this framework will support regional conservation assessments and targeted management. Moreover, by enabling the identification of fishing hotspots and detection of IUU fishing, it lays the groundwork for a broader traceability system in marine ecosystems. Much like the landmark elephant ivory tracing study, our approach has the potential to transform marine conservation globally. Graphical AbstractWe developed the Reefshark Genomescape, a genomic framework for assessing shark population health and fisheries traceability across the Indo-Pacific. Genome-wide data from grey reef and silvertip sharks revealed contrasting patterns, unexpected connectivity, and genomic signals of decline. Geographic assignment of fished individuals reached 96% accuracy, enabling detection of illegal fishing and identification of hotspots. This framework strengthens regional management, supports IUCN reassessments, and lays the foundation for global marine traceability systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/676358v2_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@1eafd3aorg.highwire.dtl.DTLVardef@96ebd1org.highwire.dtl.DTLVardef@541d02org.highwire.dtl.DTLVardef@3c9ca2_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Density-dependent network structuring within and across wild animal systems

High population density should drive individuals to more frequently share space and interact, producing better-connected spatial and social networks [1-4]. Although this theory is fundamental to our understanding of disease dynamics [2,5-8], it remains unconfirmed how local density generally drives individuals positions within their networks, which reduces our ability to understand and predict density-dependent processes [4,9,10]. Here we provide the first general evidence that density drives greater network connectedness at fine spatiotemporal scales, at the scale of individuals within wild animal populations. We analysed 36 datasets of simultaneous spatial and social behaviour in >58,000 individual animals, spanning 30 species of fish, reptiles, birds, mammals, and insects. 80% of systems exhibited strong positive relationships between local density and network centrality. However, >80% of relationships were nonlinear and 75% became shallower at higher values, signifying that demographic and behavioural processes counteract densitys effects, thereby producing saturating trends [11-15]. Densitys effect was much stronger and less saturating for spatial than social networks, such that individuals become disproportionately spatially connected rather than socially at higher densities. Consequently, ecological processes that depend on spatial connections (e.g. indirect pathogen transmission, resource competition, and territory formation) are likely more density-dependent than those involving social interactions (e.g. direct pathogen transmission, aggression, and social learning). These findings reveal fundamental ecological rules governing societal structuring, with widespread implications. Identifying scaling rules based on processes that generalise across systems, such as these patterns of density dependence, might provide the ability to predict network structures in novel systems.

ecology↗